diff --git a/conf/modules.config b/conf/modules.config
index 11c707a7..fb26908e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -38,7 +38,7 @@ process {
             path: { "${params.outdir}/cat_fastq" },
             mode: params.publish_dir_mode,
             pattern: '*.fastq',
-            // enabled: params.save_merged_fastq //TODO ? implement save_merged_fastq param
+            enabled: params.save_merged
         ]
     }
 
@@ -230,7 +230,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/mature" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_aligned_mirna_quant
         ]
     }
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:.*' {
@@ -245,7 +246,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/hairpin" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_aligned_mirna_quant
         ]
     }
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:.*' {
@@ -274,7 +276,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/seqcluster" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_aligned_mirna_quant
         ]
     }
     withName: 'MIRTOP_QUANT' {
@@ -317,7 +320,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome_quant/bam" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_aligned
         ]
     }
 
diff --git a/conf/test.config b/conf/test.config
index e699776b..e826354b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -24,8 +24,10 @@ params {
     input            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
     fasta            = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
 
-    mirtrace_species = 'hsa'
-    protocol         = 'illumina'
-    skip_mirdeep     = true
+    mirtrace_species         = 'hsa'
+    protocol                 = 'illumina'
+    skip_mirdeep             = true
+    save_merged              = false
+    save_aligned_mirna_quant = false
 
 }
diff --git a/nextflow.config b/nextflow.config
index 34d26823..850030a0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -28,6 +28,8 @@ params {
     mirgenedb_hairpin           = null
     mirgenedb_gff               = null
     mirgenedb_species           = null
+    save_aligned                = false
+    save_aligned_mirna_quant     = true
 
     // UMI handling
     with_umi                   = false
@@ -46,7 +48,7 @@ params {
     fastp_min_length            = 17
     fastp_known_mirna_adapters  = "$projectDir/assets/known_adapters.fa"
     save_trimmed_fail           = false
-    save_merged                 = false
+    save_merged                 = true
     skip_fastqc                 = false
     skip_multiqc                = false
     skip_mirdeep                = false
@@ -83,7 +85,6 @@ params {
     version                    = false
 
     // Config options
-
     custom_config_version       = 'master'
     custom_config_base          = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_description  = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9a2f84a4..15df803b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -78,7 +78,8 @@
                 "skip_umi_extract": {
                     "type": "boolean",
                     "fa_icon": "fas fa-compress-alt",
-                    "description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run."
+                    "description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run.",
+                    "default": true
                 },
                 "umitools_bc_pattern": {
                     "type": "string",
@@ -184,6 +185,16 @@
                     "help_text": "Saving generated references means that you can use them for future pipeline runs, reducing processing times.",
                     "fa_icon": "fas fa-save"
                 },
+                "save_aligned": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-download",
+                    "description": "Save aligned reads in bam format."
+                },
+                "save_aligned_mirna_quant": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Save aligned reads in bam format of miRNA quant subworkflow."
+                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
@@ -254,7 +265,8 @@
                 },
                 "save_merged": {
                     "type": "boolean",
-                    "description": "Save merged reads."
+                    "description": "Save merged reads.",
+                    "default": true
                 }
             }
         },